Attribute Manifest Name Description Required Conditional If Data Type Valid Values HTAN Biospecimen ID Biospecimen HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz) True String Source HTAN Biospecimen ID Biospecimen This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU). False String HTAN Parent ID Biospecimen HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant. True String Timepoint Label Biospecimen Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED. True String Collection Days from Index Biospecimen Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable' True String Adjacent Biospecimen IDs Biospecimen List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ... False String Biospecimen Type Biospecimen Biospecimen Type True String Tissue Biospecimen Type Blood Biospecimen Type Analyte Biospecimen Type Mouth Rinse Biospecimen Type Stool Biospecimen Type Urine Biospecimen Type Ascites Biospecimen Type Sputum Biospecimen Type Fluids Biospecimen Type Bone Marrow Biospecimen Type Cells Biospecimen Type Acquisition Method Type Biospecimen Records the method of acquisition or source for the specimen under consideration. True String Autopsy Biopsy Fine Needle Aspirate Surgical Resection Punch Biopsy Shave Biopsy Excision Re-excision Sentinel Node Biopsy Lymphadenectomy - Regional Nodes Other Acquisition Method Non induced sputum Induced sputum BAL (bronchial alveolar lavage) Cytobrush Blood draw Fluid collection Forceps biopsy Core needle biopsy Endoscopic biopsy Not specified Fixative Type Biospecimen Text term to identify the type of fixative used to preserve a tissue specimen True String Acetone Alcohol Formalin Glutaraldehyde OCT media RNAlater Saline 95% Ethanol Dimidoester Carbodiimide Dimethylacetamide Para-benzoquinone PAXgene tissue TCL lysis buffer NP40 lysis buffer Methacarn Cryo-store Carnoy's Fixative Polaxamer Other None unknown Unfixed Storage Method Biospecimen The method by which a biomaterial was stored after preservation or before another protocol was used. True String Ambient temperature Cut slide Fresh Frozen at -20C Frozen at -70C Frozen at -80C Frozen at -150C Frozen in liquid nitrogen Frozen in vapor phase Paraffin block RNAlater at 4C RNAlater at 25C RNAlater at -20C Refrigerated at 4 degrees Refrigerated vacuum chamber 4C in vacuum chamber Desiccant at 4C Not Applicable unknown Processing Days from Index Biospecimen Number of days from the research participant's index date that the biospecimen was processed. If not applicable please enter 'Not Applicable' True String Protocol Link Biospecimen Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated. True String Site Data Source Biospecimen Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed. False String Collection Media Biospecimen Material Specimen is collected into post procedure False String DMEM DMEM+Serum RPMI RPMI+Serum PBS PBS+Serum None Mounting Medium Biospecimen The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media False String Aqueous water based Non-Aqueous Solvent based Xylene Toluene Antifade with DAPI Antifade without DAPI PBS unknown Not Reported Processing Location Biospecimen Site with an HTAN center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed. False String Histology Assessment By Biospecimen Text term describing who (in what role) made the histological assessments of the sample False String Pathologist Research Scientist Other unknown Histology Assessment Medium Biospecimen The method of assessment used to characterize histology False String Digital Microscopy Other unknown Preinvasive Morphology Biospecimen Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN False String Melanocytic hyperplasia Atypical melanocytic proliferation Melanoma in situ - superficial spreading Melanoma in situ - lentigo maligna type Melanoma in situ - acral-lentiginous Melanoma in situ - arising in a giant congenital nevus Persistent melanoma in situ Melanoma in situ - not otherwise classified Scar - no residual melanoma Invasive melanoma - superficial spreading Invasive melanoma - nodular type Invasive melanoma - lentigo maligna Invasive melanoma - acral lentiginous Invasive melanoma - desmoplastic Invasive melanoma - nevoid Invasive melanoma - other Normal WDA Reserve cell hyperplasia Squamous metaplasia - mature Squamous metaplasia - immature Mild dysplasia Moderate dysplasia Severe dysplasia Squamous Carcinoma in situ Atypical adenomatous hyperplasia Adenocarcinoma in situ - non mucinous Adenocarcinoma in situ - mucinous Benign tumor NOS Hamartoma Carcinoma NOS No diagnosis possible Tumor Infiltrating Lymphocytes Biospecimen Measure of Tumor-Infiltrating Lymphocytes [Number] False String Degree of Dysplasia Biospecimen Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration. False String Normal or basal cell hyperplasia or metaplasia Mild dysplasia Moderate dysplasia Severe dysplasia Carcinoma in Situ unknown Dysplasia Fraction Biospecimen Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5] False String Number Proliferating Cells Biospecimen Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s). False String Percent Eosinophil Infiltration Biospecimen Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen. False String Percent Granulocyte Infiltration Biospecimen Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen. False String Percent Inflam Infiltration Biospecimen Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue. False String Percent Lymphocyte Infiltration Biospecimen Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen. False String Percent Monocyte Infiltration Biospecimen Numeric value to represent the percentage of monocyte infiltration in a sample or specimen. False String Percent Necrosis Biospecimen Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen. False String Percent Neutrophil Infiltration Biospecimen Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen. False String Percent Normal Cells Biospecimen Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen. False String Percent Stromal Cells Biospecimen Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc. False String Percent Tumor Cells Biospecimen Numeric value that represents the percentage of infiltration by tumor cells in a sample. False String Percent Tumor Nuclei Biospecimen Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen. False String Fiducial Marker Biospecimen Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging. False String Nuclear Stain - DAPI Fluorescent Beads Grid Slides - Hemocytometer Adhesive Markers Other unknown Not Reported Slicing Method Biospecimen Imaging specific: the method by which the tissue was sliced. False String Vibratome Cryosectioning Tissue molds Sliding microtome Sectioning Other unknown Not Reported Lysis Buffer Biospecimen scRNA-seq specific: Type of lysis buffer used False String Method of Nucleic Acid Isolation Biospecimen Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. [Text - max length 100] False String HTAN Parent Biospecimen ID Biospecimen HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated True Is lowest level is "Yes - Is lowest level" String Ischemic Time Biospecimen Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value. False Biospecimen is "Bone"' 'Biospecimen is "Analyte"' 'Biospecimen is "Tissue"' 'Biospecimen is "Urine" String Ischemic Temperature Biospecimen Specify whether specimen experienced warm or cold ischemia. False Biospecimen is "Bone"' 'Biospecimen is "Analyte"' 'Biospecimen is "Tissue"' 'Biospecimen is "Urine" String Warm Ischemia Cold Ischemia Ambient air 4C wet ice Negative -20C Dry Ice Liquid Nitrogen unknown Histologic Morphology Code Biospecimen The microscopic anatomy of normal and abnormal cells and tissues of the specimen as captured in the morphology codes of the International Classification of Diseases for Oncology, 3rd Edition (ICD-O-3). Example - 8010/0 True Biospecimen is "Bone"' 'Biospecimen is "Tissue"' 'Biospecimen is "Urine" String Preservation Method Biospecimen Text term that represents the method used to preserve the sample. True Biospecimen is "Bone"' 'Biospecimen is "Tissue"' 'Biospecimen is "Urine" String Cryopreserved Cryopreservation in liquid nitrogen - dead tissue Cryopreservation in dry ice - dead tissue Cryopreservation in liquid nitrogen - live cells Formalin fixed paraffin embedded - FFPE Formalin fixed-unbuffered Formalin fixed-buffered Fresh Fresh dissociated and single cell sorted into plates in NP40 buffer OCT Snap Frozen Frozen Negative 80 Deg C Liquid Nitrogen Fresh dissociated Fresh dissociated and single cell sorted Fresh dissociated and single cell sorted into plates Methacarn fixed paraffin embedded - MFPE unknown Not Reported Analyte Type Biospecimen The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen True Biospecimen is "Analyte" String cfDNA Analyte DNA Analyte RNA Analyte Total RNA Analyte Tissue Block Analyte Tissue Section Analyte PBMCs or Plasma or Serum Analyte cDNA Libraries Analyte PBMCs Plasma Serum Analyte lipid protein metabolite Tissue Biospecimen Type Biospecimen Tissue biospecimen False String Blood Biospecimen Type Biospecimen Blood biospecimen False String Analyte Biospecimen Type Biospecimen A molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen False String Urine Biospecimen Type Biospecimen Urine biospecimen False String Bone Marrow Biospecimen Type Biospecimen Bone Marrow biospecimen False String Fixation Duration Biospecimen The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes) True Biospecimen is "Analyte" String Slide Charge Type Biospecimen A description of the charge on the glass slide. True Biospecimen is "Analyte" String Uncharged Charged Coverslip Not applicable Other Section Thickness Value Biospecimen Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um). True Biospecimen is "Analyte" String Sectioning Days from Index Biospecimen Number of days from the research participant's index date that the biospecimen was sectioned after collection. If not applicable please enter 'Not Applicable' True Biospecimen is "Analyte" String Shipping Condition Type Biospecimen Text descriptor of the shipping environment of a biospecimen. True Biospecimen is "Analyte"' 'Biospecimen is "Blood" String Ambient Pack Cold Pack Dry Ice Ice Pack Liquid Nitrogen Specimen at Room Temperature Other Shipping Environment Not Shipped Specimen Laterality Biospecimen For tumors in paired organs, designates the side on which the specimen was obtained. True Biospecimen is "Bone"' 'Biospecimen is "Tissue"' 'Biospecimen is "Urine" String Bilateral Left Right unknown Not Reported Not Applicable Portion Weight Biospecimen Numeric value that represents the sample portion weight, measured in milligrams. False Biospecimen is "Bone"' 'Biospecimen is "Tissue"' 'Biospecimen is "Urine" String Total Volume Biospecimen Numeric value for the total amount of sample or specimen False Biospecimen is "Bone"' 'Biospecimen is "Tissue"' 'Biospecimen is "Urine" String Tumor Tissue Type Biospecimen Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint (add rows to select multiple values along with timepoints) True Biospecimen is "Bone"' 'Biospecimen is "Tissue"' 'Biospecimen is "Urine" String Additional Primary Local recurrence Metastatic Premalignant Primary Recurrent Normal Normal adjacent Normal distant Post therapy Post therapy neoadjuvant Post therapy adjuvant Not Otherwise Specified Premalignant - in situ Atypia - hyperplasia Not analyzed Biospecimen Dimension 1 Biospecimen First dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the "dimensions_unit" CDE False Biospecimen is "Bone"' 'Biospecimen is "Tissue" String Biospecimen Dimension 2 Biospecimen Second dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the "dimensions_unit" CDE False Biospecimen is "Bone"' 'Biospecimen is "Tissue" String Biospecimen Dimension 3 Biospecimen Third dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the "dimensions_unit" CDE False Biospecimen is "Bone"' 'Biospecimen is "Tissue" String Section Number in Sequence Biospecimen Numeric value (integer, including ranges) provided to a sample in a series of sections (list all adjacent sections in the Adjacent Biospecimen IDs field) False Biospecimen is "Bone"' 'Biospecimen is "Tissue" String Other Acquisition Method Biospecimen A custom acquisition method False String Acquisition Method Other Specify Biospecimen A custom acquisition method [Text - max length 100 characters] True Acquisition is "Other Acquisition Method" String Total Volume Unit Biospecimen Unit of measurement used for the total amount of sample or specimen False String mL cubic millimeter square centimeter Dimensions Unit Biospecimen Unit of measurement used for dimension CDEs in metric system (i.e. cm, mm, etc) False String mm cm Site of Resection or Biopsy Biospecimen The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O). True Biospecimen is "Bone"' 'Biospecimen is "Tissue"' 'Biospecimen is "Urine" String Abdomen NOS Abdominal esophagus Accessory sinus NOS Acoustic nerve Adrenal gland NOS Ampulla of Vater Anal canal Anterior 2/3 of tongue NOS Anterior floor of mouth Anterior mediastinum Anterior surface of epiglottis Anterior wall of bladder Anterior wall of nasopharynx Anus NOS Aortic body and other paraganglia Appendix Ascending colon Autonomic nervous system NOS Axillary tail of breast Base of tongue NOS Bladder neck Bladder NOS Blood Body of pancreas Body of penis Body of stomach Bone marrow Bone of limb NOS Bone NOS Bones of skull and face and associated joints Border of tongue Brain stem Brain NOS Branchial cleft Breast NOS Broad ligament Cardia NOS Carotid body Cauda equina Cecum Central portion of breast Cerebellum NOS Cerebral meninges Cerebrum Cervical esophagus Cervix uteri Choroid Ciliary body Cloacogenic zone Colon NOS Commissure of lip Conjunctiva Connective subcutaneous and other soft tissues of abdomen Connective subcutaneous and other soft tissues of head face and neck Connective subcutaneous and other soft tissues of lower limb and hip Connective subcutaneous and other soft tissues of pelvis Connective subcutaneous and other soft tissues of thorax Connective subcutaneous and other soft tissues of trunk NOS Connective subcutaneous and other soft tissues of upper limb and shoulder Connective subcutaneous and other soft tissues NOS Cornea NOS Corpus uteri Cortex of adrenal gland Cranial nerve NOS Craniopharyngeal duct Descended testis Descending colon Dome of bladder Dorsal surface of tongue NOS Duodenum Endocervix Endocrine gland NOS Endometrium Epididymis Esophagus NOS Ethmoid sinus Exocervix External ear External lip NOS External lower lip External upper lip Extrahepatic bile duct Eye NOS Eyelid Fallopian tube Female genital tract NOS Floor of mouth NOS Frontal lobe Frontal sinus Fundus of stomach Fundus uteri Gallbladder Gastric antrum Gastrointestinal tract NOS Glans penis Glottis Greater curvature of stomach NOS Gum NOS Hard palate Head of pancreas Head face or neck NOS Heart Hematopoietic system NOS Hepatic flexure of colon Hypopharyngeal aspect of aryepiglottic fold Hypopharynx NOS Ileum Ill-defined sites within respiratory system Intestinal tract NOS Intra-abdominal lymph nodes Intrahepatic bile duct Intrathoracic lymph nodes Islets of Langerhans Isthmus uteri Jejunum Kidney NOS Labium majus Labium minus Lacrimal gland Laryngeal cartilage Larynx NOS Lateral floor of mouth Lateral wall of bladder Lateral wall of nasopharynx Lateral wall of oropharynx Lesser curvature of stomach NOS Lingual tonsil Lip NOS Liver Long bones of lower limb and associated joints Long bones of upper limb scapula and associated joints Lower gum Lower limb NOS Lower lobe lung Lower third of esophagus Lower-inner quadrant of breast Lower-outer quadrant of breast Lung NOS Lymph node NOS Lymph nodes of axilla or arm Lymph nodes of head face and neck Lymph nodes of inguinal region or leg Lymph nodes of multiple regions Main bronchus Major salivary gland NOS Male genital organs NOS Mandible Maxillary sinus Meckel diverticulum Mediastinum NOS Medulla of adrenal gland Meninges NOS Middle ear Middle lobe lung Middle third of esophagus Mouth NOS Mucosa of lip NOS Mucosa of lower lip Mucosa of upper lip Myometrium Nasal cavity Nasopharynx NOS Nervous system NOS Nipple Occipital lobe Olfactory nerve Optic nerve Orbit NOS Oropharynx NOS Other ill-defined sites Other specified parts of female genital organs Other specified parts of male genital organs Other specified parts of pancreas Ovary Overlapping lesion of accessory sinuses Overlapping lesion of bladder Overlapping lesion of bones joints and articular cartilage Overlapping lesion of bones joints and articular cartilage of limbs Overlapping lesion of brain Overlapping lesion of brain and central nervous system Overlapping lesion of breast Overlapping lesion of cervix uteri Overlapping lesion of colon Overlapping lesion of connective subcutaneous and other soft tissues Overlapping lesion of corpus uteri Overlapping lesion of digestive system Overlapping lesion of endocrine glands and related structures Overlapping lesion of esophagus Overlapping lesion of eye and adnexa Overlapping lesion of female genital organs Overlapping lesion of floor of mouth Overlapping lesion of heart mediastinum and pleura Overlapping lesion of hypopharynx Overlapping lesion of ill-defined sites Overlapping lesion of larynx Overlapping lesion of lip Overlapping lesion of lip oral cavity and pharynx Overlapping lesion of lung Overlapping lesion of major salivary glands Overlapping lesion of male genital organs Overlapping lesion of nasopharynx Overlapping lesion of other and unspecified parts of mouth Overlapping lesion of palate Overlapping lesion of pancreas Overlapping lesion of penis Overlapping lesion of peripheral nerves and autonomic nervous system Overlapping lesion of rectum anus and anal canal Overlapping lesion of respiratory system and intrathoracic organs Overlapping lesion of retroperitoneum and peritoneum Overlapping lesion of skin Overlapping lesion of small intestine Overlapping lesion of stomach Overlapping lesion of tongue Overlapping lesion of tonsil Overlapping lesion of urinary organs Overlapping lesion of vulva Overlapping lesions of oropharynx Palate NOS Pancreas NOS Pancreatic duct Parametrium Paraspinal Parathyroid gland Paraurethral gland Parietal lobe Parotid gland Pelvic bones sacrum coccyx and associated joints Pelvic lymph nodes Pelvis NOS Penis NOS Peripheral nerves and autonomic nervous system of abdomen Peripheral nerves and autonomic nervous system of head face and neck Peripheral nerves and autonomic nervous system of lower limb and hip Peripheral nerves and autonomic nervous system of pelvis Peripheral nerves and autonomic nervous system of thorax Peripheral nerves and autonomic nervous system of trunk NOS Peripheral nerves and autonomic nervous system of upper limb and shoulder Peritoneum NOS Pharynx NOS Pineal gland Pituitary gland Placenta Pleura NOS Postcricoid region Posterior mediastinum Posterior wall of bladder Posterior wall of hypopharynx Posterior wall of nasopharynx Posterior wall of oropharynx Prepuce Prostate gland Pylorus Pyriform sinus Rectosigmoid junction Rectum NOS Renal pelvis Reticuloendothelial system NOS Retina Retromolar area Retroperitoneum Rib sternum clavicle and associated joints Round ligament Scrotum NOS Short bones of lower limb and associated joints Short bones of upper limb and associated joints Sigmoid colon Skin of lip NOS skin of lower limb and hip Skin of other and unspecified parts of face Skin of scalp and neck Skin of trunk skin of upper limb and shoulder skin NOS Small intestine NOS Soft palate NOS Specified parts of peritoneum Spermatic cord Sphenoid sinus Spinal cord Spinal meninges Spleen Splenic flexure of colon Stomach NOS Subglottis Sublingual gland Submandibular gland Superior wall of nasopharynx Supraglottis Tail of pancreas Temporal lobe Testis NOS Thoracic esophagus Thorax NOS Thymus Thyroid gland Tongue NOS Tonsil NOS Tonsillar fossa Tonsillar pillar Trachea Transverse colon Trigone of bladder Undescended testis unknown primary site Upper gum Upper limb NOS Upper lobe lung Upper respiratory tract NOS Upper third of esophagus Upper-inner quadrant of breast Upper-outer quadrant of breast Urachus Ureter Ureteric orifice Urethra Urinary system NOS Uterine adnexa Uterus NOS Uvula Vagina NOS Vallecula Ventral surface of tongue NOS Ventricle NOS Vertebral column Vestibule of mouth Vulva NOS Waldeyer ring Biliary tract NOS Cheek mucosa Clitoris Overlapping lesion of biliary tract unknown Not Reported